Digital Twins and Reproducibility

Bridging Point-and-Click COPASI Software with Open-Source and Flexible R Programming language

First Published: Mar 14, 2025

Last updated: mai 14, 2025

Bastien CHASSAGNOL |
Post-Doc
LPSM and Laval

Lilija Wehling |
Ph.D.
VPE BioMed X Institute

Atreyee Banerjee |
Ph.D.
Mainz Universität

Soria Gasparini |
Ph.D.
Heidelberg University

Sanjana Balaji Kuttae |
Ph.D.
VPE BioMed X Institute


Slides available on GitHub

Talks’ Layout

  • Types and applications of cell–cell tools. 👋
  • CCC tools pipeline 🕘
  • Review of CCC tools ⬇️

Types of Cell-Cell Communication

Cell-cell Categories

Classes of cell-cell communications cover:

CCC tools.

Main categories of cell communication. Reproduced from Fig1, Deciphering cell–cell interactions and communication from gene expression, from (armingol2021nrg?).


  • Autocrine signalling: induce a cellular response within the same cell.

  • Paracrine signalling: diffusion of signalling, secreted molecules in the external medium.

  • Juxtacrine signalling: contact-dependant, through gap junctions or membrane nanotubes.

  • Endocrine signalling: long-range intercellular communication enabled by blood-circulating hormones.

Review of CCC tools

Main categories of cell-cell tools

Phylogenetic tree of cell-cell tools

Phylogenetic tree of computational tools for inferring cell–cell interactions, from (armingol2024nrg?). Tools published as a preprint are marked with an asterisk.

Phylogenetic tree of computational tools for inferring cell–cell interactions, from (armingol2024nrg?). Tools published as a preprint are marked with an asterisk.

Conclusion

Take-Aways:

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Bibliographic References

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License rights

© 2025 Bastien CHASSAGNOL

Opinions expressed are solely my own and do not express the views of the researchers I am associated with.

This work is released under the MIT license.

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